black ninja order
by foxyfanlove
Summary: naruto running from a mob manages to find the last remains of the long gone order with the help of it's last remaining member naruto will set the ninja world on fire. this wil be yaoi but the main pairing you will have to try and figure out for your seves. this more than likly will be over powering naruto but hey with what he's been through i think he diserves it.


Chapter 1 innocence

The night was a blaze with laughter and joy in the village hidden in the leaves as lights lit up the shops and vendors selling special items for it was a special day, the tenth of October and the seventh anniversary of the night when the fourth hokage defeated the Kyuubi no Yoko unfortunately it wasn't all happiness as one small child ran through the dark back allies trying hard not to be noticed. As the child passed by an opening into the festival the light revealed the child's bright blond hair and ocean blue eyes though the child was thin and pale with three whiskers like marks on his cheeks his thin frame caused many to see him as a girl instead of a boy this boy's name is naruto uzumaki the last of the uzumaki clan and the last of an ancient order. Naruto was running through the shadows on his way to see the hokage when he heard voices up ahead stopping just before the corner he could hear the mob as they shouted trying to gain more members to come after him. Sighing naruto quickly looked around for some where he could hide until the night was over, just as he thought about continuing on to the hokage tower he saw an open grate leading to the sewers he ran to it and slipped under and into the sewers.

Naruto walked for some time before he found a small passage that had opened in the floor that was almost too small for him to fit through but when he put his hand on it he felt a breeze coming from the crack, thinking quickly he slipped into the crack an started to shimmy down further when he lost his footing and fell down into the dark as he was falling naruto closed his eyes and waited for the end when something caught him and a bright light appeared in front of him slowly opening his eyes he looked on shocked at the giant ghostly white face that appeared before him the only part of the face that looked human was the chin, nose, and mouth everything above the nose was covered in wispy hair like tentacles when naruto looked around he found that the hair continued down covering all of the thing except for what appeared to be the things belly that stretched from its head down as far as naruto could see. Looking under him naruto saw the hair had moved to catch him as he fell, when he looked back at the creature's face it smiled down at him

"Hello there young one my name is hevlaska who are you and what are you doing all the way down here?" naruto smiled up at hevlaska as she sat him down on a large platform

"I'm naruto I was hiding when I found the entrance to this place, where am i?" naruto asked hevlaska smiled

"you young naruto are in the black order or what is left of it" naruto grew even more confused and was sure it appeared on his face as hevlaska began to explain

"you see naruto over a million years ago this world was filled with a great evil known as the millennium earl who could create monsters known as Akuma though they were different to the supposed demons of today, the Akuma were weapons made by the earl from the sadness and pain a human feels when they lose someone precious to them. in their time of grieving the earl would appear before them and offered to bring them back to life if they called out the name of their loved one but instead the souls would be trapped in a metal skeleton and forced to do the earls biding. they would wear the skins of the ones who brought them back and were programed to kill in order to gain power and level up none of the human weapons could scratch them much less kill them but one day a golden cube was fond that predicted the end of human kind if the earl was to succeed the cube also told of pieces known as innocence that were scattered throughout the world when refined they could be turned into weapons to hunt Akuma, the ones that used the innocence were known as accommodators and were divided into two types the weapon ones could evolve their innocence into a special crystal type made of their blood while the parasite types could turn parts of their bodies into their anti Akuma weapons, with the cubes guidance they formed what was known as the black order to protect mankind from the Akuma unfortunately a million years ago there was a great war held between the black order and the earl for the fate of the world, knowing that they may not make it from the battle they left all their knowledge with me and if you accept I will pass on that knowledge to you" naruto looked down at his feet as he tried to process everything she had told him before he looked back at her face that waited high above him

"but why me, why would you give so much to me I just fell in here" hevlaska lifted one of her tentacle like hands that reached down for his left hand and removed the glove that covered his disfigured left arm, as the glove was removed the red skin of his arm began to show and when it was finally off there was a green cross sitting in the center of his hand

"this is why I have chosen you for you hold what is known as the heart innocence it is from this peace that all other innocence draws its power and is one of the only two pieces left in the world" as she touched the innocence in his arm a green glow covered him, when the light died down his arm was enlarged and covered in a thick grey metal like substance. His hand had had become claw like with green flames coming from his shoulder and the cross that remained in the center of his hand "I remember this innocence well it once belonged to the exorcist who defeated the millennium earl unfortunately he suffered such grave injuries that he too died, this innocence is known as the destroyer of time now tell me naruto will you accept the knowledge of the black order" naruto smiled up at hevlaska as he held his arm close to his chest

"I will" as soon as those words left his mouth hevlaska leaned down and kissed his forehead causing a blinding light to shine from them as naruto gained all of the memories from hevlaska when it ended naruto was holding his head in pain from all of the information he had received. When he finally let go of his head to say something a ribbon of black streaked across his vision before wrapping around his feet and legs turning into knee high boots as his pants were shredded into short shorts. Naruto looked down in shock as a green hexagon appeared on top of his foot as green lines raced up the sides of his legs forming green hexagons on the sides of his thighs before the same green fire on his arm flared from the hexagons. Naruto looked up at hevlaska only to see her smile down at him "hevlaska what are these?"

"these naruto are known as the dark boots and they have chosen you to be their accommodator, you naruto uzumaki are the holder of the last innocence in the world" naruto stood on the platform and walked over to the control panel before looking back at hevlaska

"I'm going to get hokage-jiji will you still be here to explain everything to him?" hevlaska nodded her head as she smiled "we can bring the black order back as the science department of the hidden leaf village" with that naruto flicked a switch on the panel causing bright lights to turn on throughout the entire facility before the platform started to rise "I'll be right back" hevlaska nodded as the platform took naruto up to the top level showing him the slightly destroyed state the headquarters was in before reaching the highest level he could reach before the destroyed levels blocked his path naruto sighed before kicking the rubble with his dark boots smashing in the wreckage only to find the next level was different than the floors before it when he saw the leaf symbol on the wall he quickly deactivated his innocence before climbing out of the hole in the floor and running to the stairs to climb higher through the floors looking for someone he knew before he finally spotted an anbu wearing the standard armor but had a snake mask, the anbu turned as naruto ran up to her

"naruto what are you doing here?" naruto smiled as she kneeled down to his level

"I need to get to the hokage you'll never believe what I've found" the anbu nodded and picked him up before disappearing in a swirl of leaves and reappearing in front of a startled old man with grey hair and beard wearing white and red robes with a pipe in his mouth

"to what do I owe the pleasure of this visit" the old man said as he looked at the anbu before he saw naruto walk up to him with a large smile on his face

"you are never going to believe what I've found hokage jiji" naruto told the hokage about how he was on his way to him when he heard a mob forming and ran to hide in the sewers were he found a small crack in the floor how he met hevlaska and all that she had told him. At the end Sarutobi looked shocked and even more so when naruto activated both of his innocence to prove that he was telling the truth and not just some lie, after a few minutes of the hokage looking over both the dark boots and the destroyer of time he sighed

"let us see this place" Sarutobi said as he held out his hand and naruto took it before the two of them and three anbu disappeared from the room appearing in the same room naruto and the snake anbu had disappeared from soon naruto was leading them down to the last floor where the four saw a massive hole in the floor that naruto was walking towards he turned to them as he reached the edge

"well are you coming" he smiled before jumping through the hole Sarutobi and the anbu got to the edge and saw a platform just under the hole that was waiting there with naruto standing by a large metal box with a lot of levers and buttons they jumped down onto the platform and naruto pressed a button then the platform began moving down. As they went they looked over the structure seeing the damage that had been done to it before they entered a bitch black chamber suddenly a ghostly white light appeared before them as naruto introduced them to hevlaska. Sarutobi turned from hevlaska to naruto

"it seems naruto that hevlaska is giving this place to you, what do you want done with it" naruto smiled at the four people in front of him all looking for an answer

"jiji dose the hidden leaf village have a science department?" Sarutobi looked confused as he shook his head negative and naruto smiled "well I was thinking with the memories I have from the members of the science division plus all of the advanced technology here we could make some of the most advanced weaponry for our ninjas but of course to make sure that it doesn't fall into the wrong hands we can get hevlaska to scan their minds completely to make sure they are one hundred percent loyal to the leaf same with the other scientists that would be working here" Sarutobi looked from naruto to hevlaska who nodded saying she would be happy to help before he nodded his head

"all right then but we will have to repair this place back to its former glory that includes the upper levels" Sarutobi thought for a minute before turning to the three anbu that had followed him there "go and get all of the anbu that are not on duty right now and bring them here" the three nodded before disappearing in a whirl wind of leaves while the hokage turned to naruto and took in the sight of his ripped clothes "we may have to do something about your clothes before they come back" naruto looked down at himself and nodded in agreement before he smiled up at the old kage

"I'll be right back" he said before he activated the dark boots and jumped off the platform, using the memories of the previous accommodator lenalee he ran through the base until he found her room and managed to find some clothes packed away that would fit him and when he looked in the mirror he blushed a little the skirt he found went just to his thighs while the slim black gloves and official exorcist jacket with the silver rose cross and silver lining combined with the dark boots and with his hair coming down to his shoulders he really looked like a girl. He shook himself out of his daze before running back through the halls and jumped onto the platform deactivating the dark boots just as about fifty anbu appeared there the hokage looked at naruto before shrugging his shoulders and turning to the anbu that he had called there

"I'm sure that your all wondering what this place is and why I have called you all here, for what this is I leave that to hevlaska to explain" the anbu looked up at hevlaska a little startled by what they were seeing as she explained about the order and what it used to do once her explanation was done they turned to the hokage again who gestured to naruto (while the anbu were listening to hevlaska naruto explained how the outfit he was wearing would allow him greater use of the dark boots and would keep the council off him if they believed that he was not the same person as his whisker marks had lessened to near invisible line) "this is naru the accommodator of the last two pieces of innocence on earth she also has all of the memories from the members of the previous black order that includes how to make and use the advance technology of their time, she has agreed to start an advanced science division here in the original black order headquarters this is an s rank secret and mission not even the council or elders are to know of this now I need ten of you to go out and collect the greatest scientific minds the village has to offer while the other forty will be here to help repair the structure and remove the debris, tenzo, bear, weasel, and dog you four will be guarding naru to make sure nothing happens to her" all of the anbu nodded before ten of them left to gather all the scientists they could while all but the four assigned to guard him left to start clearing the upper levels of debris, Sarutobi turned to naruto with a smile "I leave this place in your hands just remember to report to me every month on how everything is going" naruto smiled and nodded as the hokage left in a swirl of leaves naruto turned to the four that now stood their staring at him

"well we might as well get started at the top levels don't want anything to be thrown out that shouldn't be" naruto walked to the control panel and pressed a few buttons before the platform quickly lifted through the air and up to the top levels were they saw anbu already started on cleaning up the debris, naruto stepped off the platform with the anbu following behind him as he moved past the first few doors he stopped at one and entered when the anbu entered there was piles and stacks of books that reached to the ceiling as the entered tenzo nearly knocked down three stacks of books before naru was in front of him steadying the stacks "please don't mess with anything in this room it will take a long enough time to catalog all of the research in this room we don't really need to spend even more time trying to put it in order again all right" tenzo nodded and walked a little farther from the stacks to make sure not to disturb anything while dog looked over all the books then back at naru

"what are all these" naruto looked at him before smiling and looking at the books himself

"this room used to belong to an exorcist named lavi who was a member of the bookmen clan" bear snorted a little catching naru's eye "oh yes they may not sound very tough but in the time before chakra they had a memory so great it could rival the sharingan with its ability to memorise things all they needed was one look and they could memorise anything, the bookmen kept themselves secret to most of the world only the order and the millennium earl really knew of them it was their job to record the secret history of the world, the dealings behind wars every secret found, proven, and documented what lies before us is the history of the millennium war" the anbu looked at the books that hid the room before tenzo turned back to naru

"but if you know all of this why would you want to take such care of it?" naruto walked out of the room with the anbu following him and watching as he placed a ' do not touch' sign on the door

"the reason I want the books preserved Is because lavi didn't have time to finish the documents plus if it is not written down how will others learn of it after I am gone" naruto walked back to the platform and lowered it two levels before he got off again and marked a few doors and continued on bear looked to the rooms that naru had marked with signs though he had just gone in them

"what were those rooms you just marked? All you did was look in them" he asked naru stopped and turned to look at the three doors that he had marked before turning back to bear

"that's simple the first room was a medical room used for innocence maintenance and while it may not be needed it would be better to be safe than sorry as for the other two the first was a uniform storage for exorcists and will be used as the uniforms for the heads of the different research divisions while the second was the store room for the finder uniforms which will be the uniform for all of the others the reason I want to save them and use these uniforms is because they are made of a very durable material that was preferable when they were out hunting akuma as the level ones were little more than conscious cannons" as he explained naru had turned around and walked back to the platform with the anbu walking behind him as he lowered the platform four more levels before he stopped again and walked to what looked like the only room on that floor when they entered it there was a large glass tube on the right side that was surrounded by couches while the right was dominated by a large desk with a dark ornate chair and a giant world map behind it the walls were lined with shelves filled with books, from what they could see of the floor it was a deep purple but surrounding the desk was a scattering of papers and the desk itself was covered with high piles of paper. Deep blue almost purple curtains that separated the two areas of the room the anbu walked in carful of the papers that surrounded the desk while naru walked over to the glass tube with dog right behind him

"what was this thing used for?" naruto smiled as he left the glass tube and walked over behind the desk

"that is a special hologram device that connects with golems to see what they see this room is the director's office with that tube and golems flying around the headquarters he could keep track of everything that was going on at any given time and golems well that's actually were we're headed next" naru said as he walked out the door with the anbu close behind as he placed another sign on it and headed for the platform again were they headed down into a giant open room with large portions lifted and what looked like work stations on top of them with small lifts on the sides some were damaged but others remained intact. Naru stopped beside one that hadn't been destroyed were he jumped off and started to open drawers and cabinets as he took stock of all that was there after a while he sighed in relief and stood up before getting on the platform again "well that's a good thing there are still lots of parts to make golems with, most of them were smashed during the final battle" naruto lifted the platform back up to the upper levels were the anbu were working and a few scientists were already there waiting, naruto sighed this was going to take a long time.

(time skip 8 years)

It had been eight years since the science division had been formed and naruto had been right that it would take a while for them to complete all of the restorations but after two years of work they had managed to bring the black order back to its original glory after the first year of work the hokage had called naru aside and gave him four scrolls from his parents the first two were their most famous techniques while the second had been a letter from each naru punched down a wall when he found out that the fourth hokage was his father and that he had sealed the Kyuubi into him but was even more surprised to find out that his mother Kushina uzumaki knew of the book men as they had changed their name with the creation of chakra to uzumaki to better blend in, with the letter was a storage seal containing all of the work they had cataloged up until her death. After the restoration was completed the hokage called naru to a council meeting to deal with the civilian council and elders who had been whining and complaining about the money and anbu that were needed for the reconstruction that was a council meeting no one was about to forget anytime soon

(flash back 6 years ago)

Naru walked into the council room wearing the same type of uniform he put on the first day of reconstruction with his hair in pigtails and reaching his shoulders the council quieted down as he walked into the room before one of the elders an old man with a bandage around his head and on his arm spoke

"hokage sama who is this?" Sarutobi smirked

"this is naru the head of our science department" before he could get any further there was an interruption by a fat civilian member

"we don't have a science department" he was about to say more when a glare from the hokage and strangely all three elders shut him up before the hokage told them of the innocence and the knowledge that naru possessed as well as the restoration of the old black order that was to serve as the science department when he was finished the shinobi and elders looked intrigued while the civilians started shouting that they should sell the tech to the highest bidder before the elders started to talk about the cra to see if the innocence could be passed on while the shinobi council were just shaking their heads it went on like this for a few minutes with the hokage trying to calm them down before naru had enough and activated his arm and smashing it into the floor gaining the attention of everyone as they stared at the arm

"I will make this very simple and clear the tech I create will be for ninja purposes only if you civilians dare try to sell it to another country you will be weakening your own as for you elders innocence bonds to the soul not DNA and I only take orders from the hokage so if you try to sell the tech to another country, enact the cra on me or try to give me orders without the hokage's approval I will leave and take everything with me" naru turned and walked back out the door

(end flash back)

After that the council hadn't bothered him since. Three years of work later one of naru's body guards Itachi left killing all of his clan but his mother and the clan children naru suspected that there was more going on here than meets the eye. After six years working in the black order bear was promoted to the head of the T and I department and just a few months ago Kakashi had left as well. Naru sat on the couch in front of the looking glass as he liked to call it as he watched all of the scientists that were working on projects at the moment the first thing they had done was an armor that was near invisible and almost indestructible of course nothing else had been finished but they were getting close to quite a few of them, naru sighed as he got up and walked back to his desk were his shadow clones were working on the paper work that never seemed to end. Over the years naruto had manage to master every jutsu his parents gave him with the help of shadow clones and had even gotten quite good at seals but when it came to his innocence it was a bit harder he had managed to get to level two with the dark boots but still couldn't get to the second stage of his arm even with the use of allen's memory.

A knock at the door caught his attention and with a quick come in one of the newer scientists came in with a piece of paper and a blush on his face as naruto had grown very beautiful even without a large chest his training kept him lean and slender which only complimented his naturally feminine body and his long sun blond hair in pigtails reaching to his lower back he had often caught men in the village drooling at him which only made him shudder in disgust at what they must be thinking but he never corrected anyone as it would bring up questions about the skirt and his feminine appearance. The new scientist dressed in the normal finder uniform walked up to him and held out the paper

"this is from the toxin and antidote department it's a list of things that we're running out of and ones that the section leader would like to try" naru nodded as he looked over the paper

"I know I already sent out the shipping order" naru looked at the man who was rubbing his hands together nervously

"we know you did but the company said that the shipment got stuck in wave as the shipping tycoon is basically holding the water hostage unless you willing to pay a fortune to get your shipment" naru sighed before folding the paper and putting it in the storage seal on his right arm

"don't worry I'll talk to the hokage about this" with that naru walked out of his office and took the platform up to the exit level were the door would lead to the main lobby of the tower the few upper levels were reserved for meetings. Naru walked out the front door before activating the dark boots and jumping through the trees at an incredible speed he reached the gate in under half an hour before he turned off the dark boots and walked calmly through the village trying to ignore the looks men and women alike were giving him. Soon enough naru made it to the hokage's office and knocked on the door with a muffled come in naruto entered the room to see Sarutobi looking through the mission scrolls. He waited a few minutes before Sarutobi looked up at him with a smile

"ah naru what can I do for you" naru smiled as he unsealed the shipment paper and handed it over to the hokage who looked at it was raised eyebrows before looking back up at naru

"that is the list of ingredients that are required by the toxin and antidote department unfortunately the only company that has been able to get us these ingredients have to go through wave to get to us, now normally this wouldn't be a problem but the only way through is by paying half a fortune to the shipping tycoon in the area" Sarutobi sighed as he handed back the paper back to naru as he lifted the mission scroll that he had been looking at

"well that may explain this, a bridge builder from wave wants protection from bandits while he heads back to wave and finishes his bridge most likely this tycoon is going to go after him to keep his business high if the bridge is finished there will no longer be a need to pay such high prices, hmm we can send you and tenzo to pick up the supplies and send a team with the bridge builder to ensure his safety " naru nodded as he resealed the page tenzo came from the shadows to stand behind naru when there was a knock on the door with a quick come in from Sarutobi Kakashi and his genin team sasuke Uchiha, kiba inuzuka, and sai walked through the door

"team seven here to request a mission" Kakashi said in a bored tone while reading his little orange book while his three students were looking at naru unfortunately he didn't notice as his eyes locked onto the little orange book in kakashi's hands while Sarutobi began to sweat lightly

"ka-ka-shi" Kakashi whipped his head up so fast his genin took a step back while his one visible eye widened and he quickly hid his book

"umm, hello naru, it's nice to see you again" he unconsciously rubbed the back of his head while the hokage was trying hard to keep from laughing and failing horribly at it while the genin looked surprised that their teacher knows the girl in front of them when kiba finally asked what was on all of their minds

"Kakashi sensei who is this?" Sarutobi finally got over his laughing fit and answered before Kakashi could

"this is naru uzumaki the head of the science division here in konoha and one of the brightest minds I have ever meet, now about your mission if your sensei thinks you're ready I would like for you to take on a joint c rank mission" sasuke and sai kept calm and neutral while looking at Kakashi with kiba nearly bouncing around in joy, Kakashi looked over his students and nodded

"I think their ready" Sarutobi nodded while kiba was shouting out in excitement with akamaru yipping happily naruto chuckled lightly at them as they calmed down again, Sarutobi sighed before getting the mission scroll

"your mission is to escort naru and a bridge builder to wave you will stay there while the bridge builder finishes his bridge and naru retrieves the order from the science division her own bodyguard the anbu tenzo will also be joining you, send in tazuna please" as soon as he said it the door opened and in walked an older man with grey hair and a small beard wearing classes and carrying a large jug of sake he looked around the room

"what is this are those brats the team that is supposed to protect me" naru glared slightly at the man while team seven were giving their client death glares as the hokage sighed

"tazuna this is team seven they will be accompanying you to wave, this is naru the head of the science division here in konoha who is headed there as well to pick up some supplies that were ordered for the science division she will be accompanied by her anbu body guard so there is no way that this will not be enough protection for the two of you" tazuna nodded as he looked at naru and tenzo who stood behind her. With that they were all dismissed and tolled to meet back up at the gates for the mission in a half hour.


End file.
